Identification of actinobacillus actinomycetemcomitans antigens for use in the diagnosis, treatment, and monitoring of periodontal diseases

ABSTRACT

Antibodies, polypeptides, and polynucleotides are provided for the detection, prevention, amelioration and treatment of diseases caused by  Actinobacillus actinomycetemcomitans.

GOVERNMENT INTERESTS

This invention was made with Government support under Grant Number RO1DE 13523 awarded by the National Institutes of Health (NationalInstitute for Dental and Craniofacial Research, NIDCR). The Governmenthas certain rights in the invention.

TECHNICAL AREA OF THE INVENTION

This invention provides methods and compositions for the diagnosis,treatment, preventions, and amelioration of diseases caused byActinobacillus actinomycetemcomitans.

BACKGROUND OF THE INVENTION

Actinobacillus actinomycetemcomitans (Aa) is the principal etiologicagent of early-onset periodontitis including localized and generalizedprepubertal periodontis, localized and generalized juvenile periodontis,and rapidly progressive or refractory adult periodontitis. Currently,diagnosis of these diseases is made by X-ray analysis usually long afterthe onset of the disease and after considerable damage to the supportingbone and tissue has occurred. Tooth loss is the ultimate detrimentaleffect of destructive periodontal disease. A national survey of theUnited States revealed a prevalence of localized juvenile periodontitisof 0.53% and of generalized juvenile periodontitis of 0.13%. Loe &Brown, J. Periodontol. 62:608-616 (1991). Findings from a number ofstudies corroborate the conclusion that early-onset disease is similarin other industrialized countries and is more frequent in developingcountries. Loe & Brown, J. Periodontol. 62:608-616 (1991). Therefore,methods of early diagnosis of early-onset periodontitis, localized andgeneralized juvenile periodontis, and rapidly progressive or refractoryadult periodontitis are needed in the art. In addition, certain types ofadult periodontitis, which in general is a very common conditionaffecting over half the adult population, are likely to be caused by Aa.Furthermore, Aa can cause extra-oral diseases such as endocarditis,thyroid gland abscesses, urinary tract infections, brain abscesses, andvertebral osteomyelitis.

There are antibiotic, surgical, and mechanical therapies for thetreatment of Aa induced periodontis, but no means for prevention.Tetracycline has been widely used in the treatment of early-onsetperiodontis. There remains a concern, however, of strains developingresistance to tetracycline as well as the possibility of overgrowth ofother pathogenic microorganisms. Given the incidence of these diseases,a safe vaccine for Aa is needed. A vaccine can be, for example, amultivalent vaccine. Control of periodontal disease is also veryimportant in light of recent attention to the possible role ofperiodontal infections as risk factors for systemic disease (e.g.,coronary heart disease).

While most people have Aa as a normal member of their dental plaque, itusually does not cause disease. However, when Aa does cause disease, thehost mounts an enormous immune response that is inevitably futile,presumably because the immune response is directed against the wrong Aaantigens. Providing the most appropriate periodontal treatment requiresmaking an accurate diagnosis, performing optimum treatment, andmonitoring the patient's response to therapy.

Currently, standard microbiological tests for Aa detect only thepresence of Aa in dental plaque, and do not specifically identifydisease activity. For this reason these tests have a low positivepredictive value. Because Aa is normally found in the plaque of evenhealthy individuals, the application of these tests is limited in theirusefulness to those who present with certain clinical manifestations ofdisease, including for example, patients with advanced attachment lossand bone loss before the age of 25, patients aged about 25-35 with rapiddestruction of attachment and bone in a relatively short period of time(rapidly progressive periodontitis), and patients who continue to loseattachment despite stringent treatment (refractory periodontitis).

DNA probe technology has been developed to identify the presence of Aain dental plaque, but this technology is unable to distinguish betweenAa that is normally part of the dental plaque community and Aa that isinvolved in an actual disease process. Therefore, these DNA probes donot identify Aa involved in a disease process.

Therefore, methods of diagnosing, monitoring, treating, preventing, orameliorating a disease caused by Aa are needed in the art.

SUMMARY OF THE INVENTION

It is an object of the invention to provide methods and compositions forthe treatment, amelioration, and prevention of diseases caused by Aa.This and other objects of the invention are provided by one or more ofthe embodiments described below.

One embodiment of the invention provides a purified immunogenicpolypeptide comprising at least 5 contiguous amino acids of an aminoacid sequence selected from the group consisting of SEQ ID NO:2, SEQ IDNO:4, SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO:10, SEQ ID NO:12, SEQ IDNO:14, SEQ ID NO:16, SEQ ID NO:18, SEQ ID NO:20, SEQ ID NO:22, SEQ IDNO:24, SEQ ID NO:26, SEQ ID NO:28, SEQ ID NO:30, SEQ ID NO:32, SEQ IDNO:34, SEQ ID NO:36, SEQ ID NO:38, SEQ ID NO:40, SEQ ID NO:42, SEQ IDNO:44, SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ IDNO:54, SEQ ID NO:56, SEQ ID NO:58, SEQ ID NO:60, SEQ ID NO:62, SEQ IDNO:64, SEQ ID NO:66, SEQ ID NO:68, SEQ ID NO:70, SEQ ID NO:72, SEQ IDNO:74, SEQ ID NO:76, SEQ ID NO:78, SEQ ID NO:80, SEQ ID NO:82, SEQ IDNO:84, SEQ ID NO:86, SEQ ID NO:88, SEQ ID NO:90, SEQ ID NO:92, SEQ IDNO:94, SEQ ID NO:96, SEQ ID NO:98, SEQ ID NO:100, SEQ ID NO:102, SEQ IDNO:104, SEQ ID NO:106, SEQ ID NO:108, SEQ ID NO:110, SEQ ID NO:112, SEQID NO:114, SEQ ID NO:116, SEQ ID NO:118, SEQ ID NO:120, SEQ ID NO:122,SEQ ID NO:124, SEQ ID NO:126, SEQ ID NO:128, SEQ ID NO:130, SEQ IDNO:132, SEQ ID NO:134, SEQ ID NO:,136, SEQ ID NO:138, SEQ ID NO:140, SEQID NO:142, SEQ ID NO:144, SEQ ID NO:146, SEQ ID NO:148, SEQ ID NO:150,SEQ ID NO:152, SEQ ID NO:154, SEQ ID NO:156, SEQ ID NO:158, SEQ IDNO:160, SEQ ID NO:162, SEQ ID NO:164, SEQ ID NO:166, SEQ ID NO:168, SEQID NO:170, SEQ ID NO:172, SEQ ID NO:174, SEQ ID NO:176, SEQ ID NO:178,SEQ ID NO:180, SEQ ID NO:182, SEQ ID NO:184, SEQ ID NO:186, SEQ IDNO:188, SEQ ID NO:190, SEQ ID NO:192, SEQ ID NO:194, SEQ ID NO:196, SEQID NO:198, SEQ ID NO:200, SEQ ID NO:202, SEQ ID NO:204, SEQ ID NO:206,SEQ ID NO:208, SEQ ID NO:210, SEQ ID NO:212, SEQ ID NO:214, SEQ IDNO:216, SEQ ID NO:218, SEQ ID NO:220, SEQ ID NO:222, SEQ ID NO:224, SEQID NO:226, SEQ ID NO:228, SEQ ID NO:230, SEQ ID NO:232, and SEQ IDNO:234 (“the polypeptide SEQ IDs”). While each of these polypeptidesequences are collectively referred to as “the polypeptide SEQ IDs” andare presented together in a group, each of these sequences can beseparately considered and claimed.

Another embodiment of the invention provides a purified polypeptidecomprising an amino acid sequence selected from the group consisting of“the polypeptide SEQ IDs.”

Yet another embodiment of the invention provides a purifiedpolynucleotide comprising a sequence that encodes a “polypeptide SEQID.”

Still another embodiment of the invention provides a purifiedpolynucleotide comprising at least about 15 contiguous nucleic acids ofa sequence selected from the group consisting of SEQ ID NO:1, SEQ IDNO:3, SEQ ID NO:5, SEQ ID NO:7, SEQ ID NO:9, SEQ ID NO:I 1, SEQ IDNO:13, SEQ ID NO:15, SEQ ID NO:17, SEQ ID NO:19, SEQ ID NO:21, SEQ IDNO:23, SEQ ID NO:25, SEQ ID NO:27, SEQ ID NO:29, SEQ ID NO:31, SEQ IDNO:33, SEQ ID NO:35, SEQ ID NO:37, SEQ ID NO:39, SEQ ID NO:41, SEQ IDNO:43, SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ IDNO:53, SEQ ID NO:55, SEQ ID NO:57, SEQ ID NO:59, SEQ ID NO:61, SEQ IDNO:63, SEQ ID NO:65, SEQ ID NO:67, SEQ ID NO:69, SEQ ID NO:71, SEQ IDNO:73, SEQ ID NO:75, SEQ ID NO:77, SEQ ID NO:79, SEQ ID NO:81, SEQ IDNO:83, SEQ ID NO:85, SEQ ID NO:87, SEQ ID NO:89, SEQ ID NO:91, SEQ IDNO:93, SEQ ID NO:95, SEQ ID NO:97, SEQ ID NO:99, SEQ ID NO:101, SEQ IDNO:103, SEQ ID NO:105, SEQ ID NO:107, SEQ ID NO:109, SEQ ID NO:111, SEQID NO:113, SEQ ID NO:115, SEQ ID NO:117, SEQ ID NO:119, SEQ ID NO:121,SEQ ID NO:123, SEQ ID NO:125, SEQ ID NO:127, SEQ ID NO:129, SEQ IDNO:131, SEQ ID NO:133, SEQ ID NO:135, SEQ ID NO:137, SEQ ID NO:139, SEQID NO:141, SEQ ID NO:143, SEQ ID NO:145, SEQ ID NO:147, SEQ ID NO:149,SEQ ID NO:151, SEQ I) NO:153, SEQ ID NO:155, SEQ ID NO:157, SEQ IDNO:159, SEQ ID NO:161, SEQ ID NO:163, SEQ ID NO:165, SEQ ID NO:167, SEQID NO:169, SEQ ID NO:171, SEQ ID NO:173, SEQ ID NO:175, SEQ ID NO:177,SEQ ID NO:179, SEQ ID NO:181, SEQ ID NO:183, SEQ ID NO:185, SEQ IDNO:187, SEQ ID NO:189, SEQ ID NO:191, SEQ ID NO:193, SEQ ID NO:195, SEQID NO:197, SEQ ID NO:199, SEQ ID NO:201, SEQ ID NO:203, SEQ ID NO:205,SEQ ID NO:207, SEQ ID NO:209, SEQ ID NO:211, SEQ ID NO:213, SEQ IDNO:215, SEQ ID NO:217, SEQ ID NO:219, SEQ ID NO:221, SEQ ID NO:223, SEQID NO:225, SEQ ID NO:227, SEQ ID NO:229,SEQ ID NO:231 and SEQ ID NO:233(“the polynucleotide SEQ IDs”). While each of these polynucleotidesequences are collectively referred to as “the polynucleotide SEQ IDs”and are presented together in a group, each of these sequences can beseparately considered and claimed.

Even another embodiment of the invention provides a purifiedpolynucleotide comprising the nucleotide sequence of “the polynucleotideSEQ IDs” or degenerate variants thereof.

Another embodiment of the invention provides an expression vectorcomprising a “polynucleotide SEQ ID” operably linked to an expressioncontrol sequence. The vector can be in a cultured cell.

Still another embodiment of the invention provides an antibody or afragment thereof that specifically binds to a polypeptide of “thepolypeptide SEQ IDs.” An antibody fragment can be, for example, a Fab orF(ab′)₂ fragment. The antibody can be a monoclonal antibody or apolyclonal antibody. The antibody can be present in a pharmaceuticalcomposition along with a pharmaceutically acceptable carrier.

Yet another embodiment of the invention provides a method for treating,ameliorating, or preventing a disease caused by A.actinomycetemcomitans. The method comprises administering to an animalan antibody of the invention or fragment thereof. A disease caused by A.actinomycetemcomitans is thereby treated, ameliorated, or prevented. Adisease caused by A. actinomycetemcomitans can be selected from thegroup consisting of localized prepubertal periodontis, generalizedprepubertal periodontis, localized juvenile periodontis, generalizedjuvenile periodontis, rapidly progressive adult periodontis, refractoryadult periodontis, endiocarditis, thyroid gland abscess, urinary tractinfection, brain abscess and vertebral osteomyelitis.

Even another embodiment of the invention provides a method of detectingthe presence of A. actinomycetemcomitans or an A. actinomycetemcomitansantigen in a test sample. The method comprises contacting a test samplewith an antibody of the invention that specifically binds A.actinomycetemcomitans or an A. actinomycetemcomitans antigen underconditions that allow formation of an immunocomplex between the antibodyand the A. actinomycetemcomitans or the A. actinomycetemcomitans antigenand detecting an immunocomplex. Detection of the immunocomplex indicatesthe presence of A. actinomycetemcomitans or an A. actinomycetemcomitansantigen in the test sample. The detected A. actinomycetemcomitansantigen can be an antigen that is expressed in vivo during infection ofan animal.

Another embodiment of the invention provides a pharmaceuticalcomposition that comprises a polypeptide of the invention and apharmaceutically acceptable carrier.

Still another embodiment of the invention provides a method of elicitingan immune response. The method comprises administering a polypeptide ofthe invention to an animal, wherein an immune response is elicited.

Yet another embodiment of the invention provides a method of treating,preventing, or ameliorating a disease or infection caused by A.actinomycetemcomitans. The method comprises administering a polypeptideof the invention to an animal, wherein the disease or infection istreated, prevented, or ameliorated.

Even another embodiment of the invention provides a compositioncomprising a polynucleotide of the invention and a pharmaceuticallyacceptable carrier. The polynucleotide can be DNA. The polynucleotidecan be in a plasmid.

Another method of the invention provides a method of eliciting an immuneresponse comprising administering a purified polynucleotide of theinvention to an animal, wherein an immune response is elicited. Stillanother embodiment of the invention provides a method of treating,preventing, or ameliorating a disease or infection caused by A.actinomycetemcomitans. The method comprises administering a purifiedpolynucleotide of the invention to an animal, wherein the disease orinfection is treated, prevented, or ameliorated.

Yet another embodiment of the invention provides a method foridentifying the presence of a first A. actinomycetemcomitanspolynucleotide. The method comprises contacting a test sample suspectedof containing a first A. actinomycetemcomitans polynucleotide with asecond polynucleotide, wherein the second polynucleotide is apolynucleotide of the invention, under hybridization conditions. Ahybridized first and second polynucleotide complex is detected. Thepresence of a hybridized first and second polynucleotide indicates thepresence of a first polynucleotide in the test sample.

DETAILED DESCRIPTION OF THE INVENTION

Method of Identification of Polynucleotides and Polypeptides

A method for identifying nucleotide sequences that are important to amicroorganism's ability to cause disease has been applied to Aa, theprincipal etiologic agent of early-onset periodontitis includinglocalized prepubertal periodontis, generalized prepubertal periodontis,localized juvenile periodontis, generalized juvenile periodontis,rapidly progressive adult periodontis, and refractory adult periodontis.Aa can also cause endocarditis, thyroid gland abscess, urinary tractinfection, brain abscess and vertebral osteomyelitis. The method used toidentify polynucleotide and polypeptide sequences of the invention istermed in vivo induced antigen technology (IVIAT). See Handfield et al.,Trends Microbiol. 336:336-339 (2000); WO 01/11081.

Briefly, IVIAT comprises obtaining a sample of antibodies against Aaantigens that are expressed by Aa in vivo and in vitro and adsorbing theantibodies with cells or cellular extracts of Aa that have been grown invitro. An example of a sample of antibodies that can be used is serafrom patients who have been or are infected with Aa. The unadsorbedantibodies are isolated and are used to probe an expression library ofAa DNA. Reactive clones are isolated and the cloned fragments sequenced.

IVIAT was used to identify polynucleotides of Aa that are expressed onlywhen Aa is engaged in actually causing disease in animals, and inparticular humans. Important environmental signals that normally causeAa to turn on virulence genes during an infection are missing when thebacteria are grown in the laboratory. Therefore, many of the besttargets for diagnostic and vaccine strategies were unknown. IVIATmethodology was used to identify polynucleotides that are specificallyturned on during growth of Aa in a human host and not during routinelaboratory growth. These polynucleotides and corresponding polypeptidesand antibodies are useful in developing diagnostic tests for Aa toidentify, for example, subjects who are in early stages of infection andfor monitoring response to therapy, and for developing vaccines ortreatments to prevent or treat diseases caused by Aa in susceptibleanimals.

Aa antigens identified by IVIAT have a high predictive value with regardto diseases caused by Aa, for example, periodontal diseases. Diagnostictests for Aa can be useful in applications such as screening childrenwhose mothers have a history of periodontis to determine if the childrenhave acquired a predisposition for the disease. Diseases known to beassociated with periodontitis before puberty include Papillon-Lefevresyndrome (PLS), hypophosphatasia, neutropenias, leukocyte adhesiondeficiency (LAD), Chediak-Higashi syndrome, Down's syndrome, leukemia,histiocytosis X, early-onset Type I diabetes, and acrodynia. Childrenwith these diseases are candidates for Aa testing. Additionally, otherpreadolescent children who are less prone to periodontis would benefitfrom an Aa diagnostic test since there are no other predictors or knownrisk factors.

Polypeptides

Purified polypeptides of the invention can either be full-lengthpolypeptides or fragments of polypeptides. For example, fragments ofpolypeptides of the invention can comprise about 5, 10, 25, 50, 100, or200 amino acids of polypeptides of the invention. Examples ofpolypeptides of the invention include those shown in SEQ ID NO:2, SEQ IDNO:4, SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO:10, SEQ ID NO:12, SEQ IDNO:14, SEQ ID NO:16, SEQ ID NO:18, SEQ ID NO:20, SEQ ID NO:22, SEQ IDNO:24, SEQ ID NO:26, SEQ ID NO:28, SEQ ID NO:30, SEQ ID NO:32, SEQ IDNO:34, SEQ ID NO:36, SEQ ID NO:38, SEQ ID NO:40, SEQ ID NO:42, SEQ IDNO:44, SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ IDNO:54, SEQ ID NO:56, SEQ ID NO:58, SEQ ID NO:60, SEQ ID NO:62, SEQ IDNO:64, SEQ ID NO:66, SEQ ID NO:68, SEQ ID NO:70, SEQ ID NO:72, SEQ IDNO:74, SEQ ID NO:76, SEQ ID NO:78, SEQ ID NO:80, SEQ ID NO:82, SEQ IDNO:84, SEQ ID NO:86, SEQ ID NO:88, SEQ ID NO:90, SEQ ID NO:92, SEQ IDNO:94, SEQ ID NO:96, SEQ ID NO:98, SEQ ID NO:100, SEQ ID NO:102, SEQ IDNO:104, SEQ ID NO:106, SEQ ID NO:108, SEQ ID NO:110, SEQ ID NO:112, SEQID NO:114, SEQ ID NO:116, SEQ ID NO:118, SEQ ID NO:120, SEQ ID NO:122,SEQ ID NO:124, SEQ ID NO:126, SEQ ID NO:128, SEQ ID NO:130, SEQ IDNO:132, SEQ ID NO:134, SEQ ID NO:136, SEQ ID NO:138, SEQ ID NO:140, SEQID NO:142, SEQ ID NO:144, SEQ ID NO:146, SEQ ID NO:148, SEQ ID NO:150,SEQ ID NO:152, SEQ ID NO:154, SEQ ID NO:156, SEQ ID NO:158, SEQ IDNO:160, SEQ ID NO:162, SEQ ID NO:164, SEQ ID NO:166, SEQ ID NO:168, SEQID NO:170, SEQ ID NO:172, SEQ ID NO:174, SEQ ID NO:176, SEQ ID NO:178,SEQ ID NO:180, SEQ ID NO:182, SEQ ID NO:184, SEQ ID NO:186, SEQ IDNO:188, SEQ ID NO:190, SEQ ID NO:192, SEQ ID NO:194, SEQ ID NO:196, SEQID NO:198, SEQ ID NO:200, SEQ ID NO:202, SEQ ID NO:204, SEQ ID NO:206,SEQ ID NO:208, SEQ ID NO:210, SEQ ID NO:212, SEQ ID NO:214, SEQ IDNO:216, SEQ ID NO:218, SEQ ID NO:220, SEQ ID NO:222, SEQ ID NO:224, SEQID NO:226, SEQ ID NO:228, SEQ ID NO:230, SEQ ID NO:232, and SEQ IDNO:234. These polypeptides will be referred to as “the polypeptide SEQIDs.” Homologous amino acid sequences that are at least about 75, orabout 90, 96, 98, or 99% identical to the polypeptide sequences shown inthe polypeptide SEQ IDs are also Aa polypeptides. Homologous amino acidsequences retain biological activity, i.e., are biologically functionalequivalents.

Percent sequence identity has an art recognized meaning and there are anumber of methods to measure identity between two polypeptide orpolynucleotide sequences. See, e.g., Lesk, Ed., Computational MolecularBiology, Oxford University Press, New York, (1988); Smith, Ed.,Biocomputing: Informatics And Genome Projects, Academic Press, New York,(1993); Griffin & Griffin, Eds., Computer Analysis Of Sequence Data,Part I, Humana Press, New Jersey, (1994); von Heinje, Sequence AnalysisIn Molecular Biology, Academic Press, (1987); and Gribskov & Devereux,Eds., Sequence Analysis Primer, M Stockton Press, New York, (1991).Methods for aligning polynucleotides or polypeptides are codified incomputer programs, including the GCG program package (Devereux et al.,Nuc. Acids Res. 12:387 (1984)), BLASTP, BLASTN, FASTA (Atschul et al.,J. Molec. Biol. 215:403 (1990)), and Bestfit program (Wisconsin SequenceAnalysis Package, Version 8 for Unix, Genetics Computer Group,University Research Park, 575 Science Drive, Madison, Wis. 53711) whichuses the local homology algorithm of Smith and Waterman (Adv. App.Math., 2:482-489 (1981)). For example, the computer program ALIGN whichemploys the FASTA algorithm can be used, with an affine gap search witha gap open penalty of −12 and a gap extension penalty of −2.

When using any of the sequence alignment programs to determine whether aparticular sequence is, for instance, about 95% identical to a referencesequence, the parameters are set such that the percentage of identity iscalculated over the full length of the reference polynucleotide and thatgaps in identity of up to 5% of the total number of nucleotides in thereference polynucleotide are allowed.

Variants of polypeptides shown in the polypeptide SEQ IDs and fragmentsthereof are also included in the invention. A variant is a polypeptidethat differs from a polypeptide SEQ ID or fragment thereof, only inconservative substitutions and/or modifications, such that the antigenicproperties of the polypeptide are substantially the same as the originalpolypeptide. Variants can generally be identified by modifying one ofthe polypeptide sequences of the invention, and evaluating the antigenicproperties of the modified polypeptide using, for example, animmunohistochemical assay, an enzyme-linked immunosorbant assay (ELISA),a radioimmunoassay (RIA), or a western blot assay. Polypeptides of theinvention can comprise at least 1, 5, 10, 25, 50, or 100 conservativeamino acid substitutions.

A conservative substitution is one in which an amino acid is substitutedfor another amino acid that has similar properties, such that oneskilled in the art of peptide chemistry would expect the secondarystructure and hydropathic nature of the polypeptide to be substantiallyunchanged. In general, the following groups of amino acids representconservative changes: (1) ala, pro, gly, glu, asp, gln, asn, ser, thr;(2) cys, ser, tyr, thr; (3) val, ile, leu, met, ala, phe; (4) lys, arg,his; and (5) phe, tyr, trp, his.

Variants can also (or alternatively) be modified by, for example, thedeletion or addition of amino acids that have minimal influence on theantigenic properties, secondary structure and hydropathic nature of thepolypeptide. For example, a polypeptide can be conjugated to a signal(or leader) sequence at the N-terminal end of the protein whichco-translationally or post-translationally directs transfer of theprotein. The polypeptide can also be conjugated to a linker or othersequence for ease of synthesis, purification or identification of thepolypeptide (e.g., poly-His), or to enhance binding of the polypeptideto a solid support. For example, a polypeptide can be conjugated to animmunoglobulin Fc region.

Polypeptides of the invention further comprise biologically functionalequivalents of at least about 5, 10, 25, 50, 100, or 200 amino acids ofthe polypeptides shown in the polypeptide SEQ IDs. A polypeptide is abiological equivalent if it reacts substantially the same as apolypeptide of the invention in an assay such as an immunohistochemicalassay, an ELISA, an RIA, or a western blot assay, e.g. has 90-110% ofthe activity of the original polypeptide. In one embodiment, the assayis a competition assay wherein the biologically equivalent polypeptideis capable of reducing binding of the polypeptide of the invention to acorresponding reactive antigen or antibody by about 80, 95, 99, or 100%.

Polypeptides of the invention can comprise an antigen that is recognizedby an antibody reactive against Aa. The antigen can comprise one or moreepitopes (or antigenic determinants). An epitope can be a linearepitope, sequential epitope or a conformational epitope. Epitopes withina polypeptide of the invention can be identified by several methods.See, e.g., U.S. Pat. No. 4,554,101; Jameson & Wolf, CABIOS4:181-186(1988). For example, a polypeptide of the invention can beisolated and screened. A series of short peptides, which together spanan entire polypeptide sequence, can be prepared by proteolytic cleavage.By starting with, for example, 100-mer polypeptide fragments, eachfragment can be tested for the presence of epitopes recognized in anELISA. For example, in an ELISA assay an Aa polypeptide, such as a100-mer polypeptide fragment, is attached to a solid support, such asthe wells of a plastic multi-well plate. A population of antibodies arelabeled, added to the solid support and allowed to bind to the unlabeledantigen, under conditions where non-specific adsorbtion is blocked, andany unbound antibody and other proteins are washed away. Antibodybinding is detected by, for example, a reaction that converts acolorless substrate into a colored reaction product. Progressivelysmaller and overlapping fragments can then be tested from an identified100-mer to map the epitope of interest.

A polypeptide of the invention can be produced recombinantly. Apolynucleotide encoding a polypeptide of the invention can be introducedinto a recombinant expression vector, which can be expressed in asuitable expression host cell system using techniques well known in theart. A variety of bacterial, yeast, plant, mammalian, and insectexpression systems are available in the art and any such expressionsystem can be used. Optionally, a polynucleotide encoding a polypeptidecan be translated in a cell-free translation system. A polypeptide canalso be chemically synthesized.

If desired, a polypeptide can be produced as a fusion protein, which canalso contain other amino acid sequences, such as amino acid linkers orsignal sequences, as well as ligands useful in protein purification,such as glutathione-S-transferase, histidine tag, and staphylococcalprotein A. More than one polypeptide of the invention can be present ina fusion protein.

Polynucleotides

Polynucleotides of the invention contain less than an entire microbialgenome and can be single- or double-stranded DNA or RNA. Thepolynucleotides can be purified free of other components, such asproteins and lipids. The polynucleotides of the invention encode thepolypeptides described above. Polynucleotides of the invention can alsocomprise other nucleotide sequences, such as sequences coding forlinkers, signal sequences, heterologous signal sequences, TMR stoptransfer sequences, transmembrane domains, or ligands useful in proteinpurification such as glutathione-S-transferase, histidine tag, andstaphylococcal protein A.

Polynucleotides of the invention are shown in SEQ ID NO:1, SEQ ID NO:3,SEQ ID NO:5, SEQ ID NO:7, SEQ ID NO:9, SEQ ID NO:11, SEQ ID NO:13, SEQID NO:15, SEQ ID NO:17, SEQ ID NO:19, SEQ ID NO:21, SEQ ID NO:23, SEQ IDNO:25, SEQ ID NO:27, SEQ ID NO:29, SEQ ID NO:3 1, SEQ ID NO:33, SEQ IDNO:35, SEQ ID NO:37, SEQ ID NO:39, SEQ ID NO:41, SEQ ID NO:43, SEQ IDNO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53, SEQ IDNO:55, SEQ ID NO:57, SEQ ID NO:59, SEQ ID NO:61, SEQ ID NO:63, SEQ IDNO:65, SEQ ID NO:67, SEQ ID NO:69, SEQ ID NO:71, SEQ ID NO:73, SEQ IDNO:75, SEQ ID NO:77, SEQ ID NO:79, SEQ ID NO:81, SEQ ID NO:83, SEQ IDNO:85, SEQ ID NO:87, SEQ ID NO:89, SEQ ID NO:91, SEQ ID NO:93, SEQ IDNO:95, SEQ ID NO:97, SEQ ID NO:99, SEQ ID NO:101, SEQ ID NO:103, SEQ IDNO:105, SEQ ID NO:107, SEQ ID NO:109, SEQ ID NO:111, SEQ ID NO:113, SEQID NO:115, SEQ ID NO:117, SEQ ID NO:119, SEQ ID NO:121, SEQ ID NO:123,SEQ ID NO:125, SEQ ID NO:127, SEQ ID NO:129, SEQ ID NO:131, SEQ IDNO:133, SEQ ID NO:135, SEQ ID NO:137, SEQ ID NO:139, SEQ ID NO:141, SEQID NO:143, SEQ ID NO:145, SEQ ID NO:147, SEQ ID NO:149, SEQ ID NO:151,SEQ ID NO:153, SEQ ID NO:155, SEQ ID NO:157, SEQ ID NO:159, SEQ IDNO:161, SEQ ID NO:163, SEQ ID NO:165, SEQ ID NO:167, SEQ ID NO:169, SEQID NO:171, SEQ ID NO:173, SEQ ID NO:175, SEQ ID NO:177, SEQ ID NO:179,SEQ ID NO:181, SEQ ID NO:183, SEQ ID NO:185, SEQ ID NO:187, SEQ IDNO:189, SEQ ID NO:191, SEQ ID NO:193, SEQ ID NO:195, SEQ ID NO:197, SEQID NO:199, SEQ ID NO:201, SEQ ID NO:203, SEQ ID NO:205, SEQ ID NO:207,SEQ ID NO:209, SEQ ID NO:211, SEQ ID NO:213, SEQ ID NO:215, SEQ IDNO:217, SEQ ID NO:219, SEQ ID NO:221, SEQ ID NO:223, SEQ ID NO:225, SEQID NO:227, SEQ ID NO:229, SEQ ID NO:231, and SEQ ID NO:233. Thesepolynucleotides will be referred to as the “polynucleotide SEQ IDs.”

Degenerate nucleotide sequences encoding polypeptides of the invention,as well as homologous nucleotide sequences that are at least about 75,or about 90, 96, 98, or 99% identical to the nucleotide sequences shownin the polynucleotide SEQ IDs and the complements thereof are alsopolynucleotides of the invention. Percent sequence identity can becalculated as described in the “Polypeptides” section. Degeneratenucleotide sequences are polynucleotides that encode a polypeptide shownin the polypeptide SEQ IDs or fragments thereof, but differ in nucleicacid sequence from the sequence given in the polynucleotide SEQ IDs, dueto the degeneracy of the genetic code. Complementary DNA (cDNA)molecules, species homologs, and variants of Aa polynucleotides thatencode biologically functional Aa polypeptides also are Aapolynucleotides. A polynucleotide of the invention can comprise about 5,10, 15, 50, 100, or 200 nucleotides of a nucleic acid sequence shown inthe polynucleotide SEQ IDs.

Polynucleotides of the invention can be isolated from nucleic acidsequences present in, for example, a biological sample, such as plaque,saliva, crevicular fluid, sputum, blood, serum, plasma, urine, feces,cerebrospinal fluid, amniotic fluid, wound exudate, or tissue, from aninfected individual. Polynucleotides can also be synthesized in thelaboratory, for example, using an automatic synthesizer. Anamplification method such as PCR can be used to amplify polynucleotidesfrom either genomic DNA or cDNA encoding the polypeptides.

Polynucleotides of the invention can comprise coding sequences fornaturally occurring polypeptides or can encode altered sequences whichdo not occur in nature. If desired, polynucleotides can be cloned intoan expression vector comprising expression control elements, includingfor example, origins of replication, promoters, enhancers, or otherregulatory elements that drive expression of the polynucleotides of theinvention in host cells. An expression vector can be, for example, aplasmid, such as pBR322, pUC, or ColE1, or an adenovirus vector, such asan adenovirus Type 2 vector or Type 5 vector. Optionally, other vectorscan be used, including but not limited to Sindbis virus, simian virus40, alphavirus vectors, poxvirus vectors, and cytomegalovirus andretroviral vectors, such as murine sarcoma virus, mouse mammary tumorvirus, Moloney murine leukemia virus, and Rous sarcoma virus.Minichromosomes such as MC and MC 1, bacteriophages, phagemids, yeastartificial chromosomes, bacterial artificial chromosomes, virusparticles, virus-like particles, cosmids (plasmids into which phagelambda cos sites have been inserted) and replicons (genetic elementsthat are capable of replication under their own control in a cell) canalso be used.

Methods for preparing polynucleotides operably linked to an expressioncontrol sequence and expressing them in a host cell are well-known inthe art. See, e.g., U.S. Pat. No. 4,366,246. A polynucleotide of theinvention is operably linked when it is positioned adjacent to one ormore expression control elements, which direct transcription and/ortranslation of the polynucleotide.

A vector comprising a polynucleotide of the invention can be transformedinto, for example, bacterial, yeast, insect, or mammalian cells so thatthe polypeptides of the invention can be expressed in and isolated fromcell culture. Any of those techniques that are available in the art canbe used to introduce polynucleotides into the host cells. These include,but are not limited to, transfection with naked or encapsulated nucleicacids, cellular fusion, protoplast fusion, viral infection, andelectroporation.

Polynucleotides of the invention can be used, for example, as probes orprimers, for example PCR primers, to detect the presence of Aapolynucleotides in a sample, such as a biological sample. The ability ofsuch probes and primers to specifically hybridize to Aa polynucleotidesequences will enable them to be of use in detecting the presence ofcomplementary sequences in a given sample. Polynucleotide probes andprimers of the invention can hybridize to complementary sequences in asample such as a biological sample, including plaque, saliva, crevicularfluid, sputum, blood, urine, feces, cerebrospinal fluid, amniotic fluid,wound exudate, or tissue. Polynucleotides from the sample can be, forexample, subjected to gel electrophoresis or other size separationtechniques or can be immobilized without size separation. Thepolynucleotide probes or primers can be labeled. Suitable labels, andmethods for labeling probes and primers are known in the art, andinclude, for example, radioactive labels incorporated by nicktranslation or by kinase, biotin labels, fluorescent labels,chemiluminescent labels, bioluminescent labels, metal chelator labelsand enzyme labels. The polynucleotides from the sample are contactedwith the probes or primers under hybridization conditions of suitablestringencies.

Depending on the application, varying conditions of hybridization can beused to achieve varying degrees of selectivity of the probe or primertowards the target sequence. For applications requiring highselectivity, relatively stringent conditions can be used, such as lowsalt and/or high temperature conditions, such as provided by a saltconcentration of from about 0.02 M to about 0.15 M salt at temperaturesof from about 50° C. to about 70° C. For applications requiring lessselectivity, less stringent hybridization conditions can be used. Forexample, salt conditions from about 0.14 M to about 0.9M salt, attemperatures ranging form about 20° C. to about 55° C. The presence of ahybridized complex comprising the probe or primer and a complementarypolynucleotide from the test sample indicates the presence of Aa or anAa polynucleotide sequence in the sample.

Antibodies

Antibodies of the invention are antibody molecules that specifically andstably bind to an Aa polypeptide of the invention or fragment thereof.An antibody of the invention can be a polyclonal antibody, a monoclonalantibody, a single chain antibody (scFv), or a fragment of an antibody.Fragments of antibodies are a portion of an intact antibody comprisingthe antigen binding site or variable region of an intact antibody,wherein the portion is free of the constant heavy chain domains of theFc region of the intact antibody. Examples of antibody fragments includeFab, Fab′, Fab′-SH, F(ab′)₂ and F_(v) fragments.

An antibody of the invention can be any antibody class, including forexample, IgG, IgM, IgA, IgD and IgE. An antibody or fragment thereofbinds to an epitope of a polypeptide of the invention. An antibody canbe made in vivo in suitable laboratory animals or in vitro usingrecombinant DNA techniques. Means for preparing and characterizingantibodies are well know in the art. See, e.g., Dean, Methods Mol. Biol.80:23-37 (1998); Dean, Methods Mol. Biol. 32:361-79 (1994); Baileg,Methods Mol. Biol. 32:381-88 (1994); Gullick, Methods Mol. Biol.32:389-99 (1994); Drenckhahn et al. Methods Cell. Biol. 37:7-56 (1993);Morrison, Ann. Rev. Immunol. 10:239-65 (1992); Wright et al. Crit. Rev.Immunol. 12:125-68(1992). For example, polyclonal antibodies can beproduced by administering a polypeptide of the invention to an animal,such as a human or other primate, mouse, rat, rabbit, guinea pig, goat,pig, cow, sheep, donkey, or horse. Serum from the immunized animal iscollected and the antibodies are purified from the plasma by, forexample, precipitation with ammonium sulfate, followed bychromatography, such as affinity chromatography. Techniques forproducing and processing polyclonal antibodies are known in the art.

Additionally, monoclonal antibodies directed against epitopes present ona polypeptide of the invention can also be readily produced. Forexample, normal B cells from a mammal, such as a mouse, which wasimmunized with a polypeptide of the invention can be fused with, forexample, HAT-sensitive mouse myeloma cells to produce hybridomas.Hybridomas producing Aa-specific antibodies can be identified using RIAor ELISA and isolated by cloning in semi-solid agar or by limitingdilution. Clones producing Aa-specific antibodies are isolated byanother round of screening. Monoclonal antibodies can be screened forspecificity using standard techniques, for example, by binding apolypeptide of the invention to a microtiter plate and measuring bindingof the monoclonal antibody by an ELISA assay. Techniques for producingand processing monoclonal antibodies are known in the art. See e.g.,Kohler & Milstein, Nature, 256:495 (1975). Particular isotypes of amonoclonal antibody can be prepared directly, by selecting from theinitial fusion, or prepared secondarily, from a parental hybridomasecreting a monoclonal antibody of a different isotype by using a sibselection technique to isolate class-switch variants. See Steplewski etal., P.N.A.S. U.S.A. 82:8653 1985; Spria et al., J. Immunolog. Meth.74:307, 1984. Monoclonal antibodies of the invention can also berecombinant monoclonal antibodies. See, e.g., U.S. Pat. No. 4,474,893;U.S. Pat. No. 4,816,567. Antibodies of the invention can also bechemically constructed. See, e.g., U.S. Pat. No. 4,676,980.

Antibodies of the invention can be chimeric (see, e.g., U.S. Pat. No.5,482,856), humanized (see, e.g., Jones et al., Nature 321:522 (1986);Reichmann et al., Nature 332:323 (1988); Presta, Curr. Op. Struct. Biol.2:593 (1992)), or human antibodies. Human antibodies can be made by, forexample, direct immortilization, phage display, transgenic mice, or aTrimera methodology, see e.g., Reisener et al., Trends Biotechnol.16:242-246 (1998).

Antibodies, either monoclonal and polyclonal, which are directed againstAa antigens, are particularly useful for detecting the presence of Aa orAa antigens in a sample, such as a serum sample from an Aa-infectedhuman. An immunoassay for Aa or an Aa antigen can utilize one, antibodyor several antibodies. An immunoassay for Aa or an Aa antigen can use,for example, a. monoclonal antibody directed towards an Aa epitope, acombination of monoclonal antibodies directed towards epitopes of one Aapolypeptide, monoclonal antibodies directed towards epitopes ofdifferent Aa polypeptides, polyclonal antibodies directed towards thesame Aa antigen, polyclonal antibodies directed towards different Aaantigens, or a combination of monoclonal and polyclonal antibodies.Immunoassay protocols can be based upon, for example, competition,direct reaction, or sandwich type assays using, for example, labeledantibody. Antibodies of the invention can be labeled with any type oflabel known in the art, including, for example, fluorescent,chemiluminescent, radioactive, enzyme, colloidal metal, radioisotope andbioluminescent labels.

Antibodies of the invention or fragments thereof can be bound to asupport and used to detect the presence of Aa or an Aa antigen. Supportsinclude, for example, glass, polystyrene, polypropylene, polyethylene,dextran, nylon, amylases, natural and modified celluloses,polyacrylamides, agaroses and magletite.

Polyclonal or monoclonal antibodies of the invention can further be usedto isolate Aa organisms or Aa antigens by immunoaffinity columns. Theantibodies can be affixed to a solid support by, for example, adsorbtionor by covalent linkage so that the antibodies retain theirimmunoselective activity. Optionally, spacer groups can be included sothat the antigen binding site of the antibody remains accessible. Theimmobilized antibodies can then be used to bind Aa organisms or Aaantigens from a sample, such as a biological sample including saliva,plaque, crevicular fluid, sputum, blood, urine, feces, cerebrospinalfluid, amniotic fluid, wound exudate, or tissue. The bound Aa organismsor Aa antigens are recovered from the column matrix by, for example, achange in pH.

Antibodies of the invention can also be used in immunolocalizationstudies to analyze the presence and distribution of a polypeptide of theinvention during various cellular events or physiological conditions.Antibodies can also be used to identify molecules involved in passiveimmunization and to identify molecules involved in the biosynthesis ofnon-protein antigens. Identification of such molecules can be useful invaccine development. Antibodies of the invention, including, forexample, monoclonal antibodies and single chain antibodies, can be usedto monitor the course of amelioration of a disease caused by Aa. Bymeasuring the increase or decrease of Aa antibodies to Aa proteins in atest sample from an animal, it can be determined whether a particulartherapeutic regiment aimed at ameliorating the disorder is effective.Antibodies can be detected and/or quantified using for example, directbinding assays such as RIA, ELISA, or western blot assays.

An antibody of the invention can be used in a method of the diagnosis ofAa infection by obtaining a test sample from an animal suspected ofhaving an Aa infection. The test sample is contacted with an antibody ofthe invention under conditions enabling the formation of anantibody-antigen complex (i.e., an immunocomplex). The amount ofantibody-antigen complexes can be determined by methodology known in theart. A level that is higher than that formed in a control sampleindicates an Aa infection. Alternatively, a polypeptide of the inventioncan be contacted with a test sample. Aa antibodies in a positive bodysample will form an antigen-antibody complex under suitable conditions.The amount of antibody-antigen complexes can be determined by methodsknown in the art.

Methods of Treatment, Amelioration, or Prevention of a Disease Caused byAa

Polypeptides, polynucleotides, and antibodies of the invention can beused to treat, ameliorate, or prevent a disease caused by Aa, such asearly-onset periodontitis including localized and generalizedprepubertal periodontis, localized and generalized juvenile periodontis,and rapidly progressive or refractory adult periodontitis, endocarditis,thyroid gland abscesses, urinary tract infections, brain abscesses, andvertebral osteomyelitis.

For example, an antibody, such as a monoclonal antibody of the inventionor fragments thereof, can be administered to an animal, such as a human.In one embodiment of the invention an antibody or fragment thereof isadministered to an animal in a pharmaceutical composition comprising apharmaceutically acceptable carrier. A pharmaceutical compositioncomprises a therapeutically effective amount of an antibody or fragmentsthereof. A therapeutically effective amount is an amount effective inalleviating the symptoms of Aa infection or in reducing the amount of Aaorganisms in a subject.

Polypeptides or polynucleotides of the invention can be used to elicitan immune response in a host. An immonogenic polypeptide orpolynucleotide is a polypeptide or polynucleotide of the invention thatis capable of inducing an immune response in an animal. An immunogenicpolypeptide or polynucleotide of the invention is particularly useful insensitizing an immune system of an animal such that, as one result, animmune response is produced that ameliorates or prevents the effect ofAa infection. The elicitation of an immune response in animal model canbe useful to determine, for example, optimal doses or administrationroutes. Elicitation of an immune response can also be used to treat,prevent, or ameliorate a disease or infection caused by Aa. An immuneresponse includes humoral immune responses or cell mediated immuneresponses, or a combination thereof. An immune response can alsocomprise the promotion of a generalized host response, e.g., bypromoting the production of defensins.

The generation of an antibody titer by an animal against Aa can beimportant in protection from infection and clearance of infection.Detection and/or quantification of antibody titers after delivery of apolypeptide or polynucleotide can be used to identify epitopes that areparticularly effective at eliciting antibody titers. Epitopesresponsible for a strong antibody response to Aa can be identified byeliciting antibodies directed against Aa polypeptides of differentlengths. Antibodies elicited by a particular polypeptide epitope canthen be tested using, for example, an ELISA assay to determine whichpolypeptides contain epitopes that are most effective at generating astrong response. Polypeptides or fusion proteins that contain theseepitopes or polynucleotides encoding the epitopes can then beconstructed and used to elicit a strong antibody response.

A polypeptide, polynucleotide, or antibody of the invention can beadministered to a mammal, such as a mouse, rabbit, guinea pig, macaque,baboon, chimpanzee, human, cow, sheep, pig, horse, dog, cat, or toanimals such as chickens or ducks, to elicit antibodies in vivo.Injection of a polynucleotide has the practical advantages of simplicityof construction and modification. Further, injection of a polynucleotideresults in the synthesis of a polypeptide in the host. Thus, thepolypeptide is presented to the host immune system with nativepost-translational modifications, structure, and conformation. Apolynucleotide can be delivered to a subject as “naked DNA.”

Administration of a polynucleotide, polypeptide, or antibody can be byany means known in the art, including intramuscular, intravenous,intrapulmonary, intramuscular, intradermal, intraperitoneal, orsubcutaneous injection, aerosol, intranasal, infusion pump, suppository,mucosal, topical, and oral, including injection using a biologicalballistic gun (“gene gun”). A polynucleotide, polypeptide, or antibodycan be accompanied by a protein carrier for oral administration. Acombination of administration methods can also be used to elicit animmune response. Antibodies can be administered at a daily dose of about0.5 mg to about 200 mg. In one embodiment of the invention antibodiesare administered at a daily dose of about 20 to about 100 mg.

Pharmaceutically acceptable carriers and diluents for therapeutic useare well known in the art and are described in, for example, Remington'sPharmaceutical Sciences, Mack Publishing Co. (A. R. Gennaro ed. (1985)).The carrier should not itself induce the production of antibodiesharmful to the host. Such carriers include, but are not limited to,large, slowly metabolized, macromolecules, such as proteins,polysaccharides such as latex functionalized sepharose, agarose,cellulose, cellulose beads and the like, polylactic acids, polyglycolicacids, polymeric amino acids such as polyglutamic acid, polylysine, andthe like, amino acid copolymers, peptoids, lipitoids, and inactive,avirulent virus particles or bacterial cells. Liposomes, hydrogels,cyclodextrins, biodegradable nanocapsules, and bioadhesives can also beused as a carrier for a composition of the invention.

Pharmaceutically acceptable salts can also be used in compositions ofthe invention, for example, mineral salts such as hydrochlorides,hydrobromides, phosphates, or sulfates, as well as salts of organicacids such as acetates, proprionates, malonates, or benzoates.Especially useful protein substrates are serum albumins, keyhole limpethemocyanin, immunoglobulin molecules, thyroglobulin, ovalbumin, tetanustoxoid, and other proteins well known to those of skill in the art.Compositions of the invention can also contain liquids or excipients,such as water, saline, phosphate buffered saline, Ringer's solution,Hank's solution, glucose, glycerol, dextrose, malodextrin, ethanol, orthe like, singly or in combination, as well as substances such aswetting agents, emulsifying agents, tonicity adjusting agents,detergent, or pH buffering agents. Additional active agents, such asbacteriocidal agents can also be used.

If desired, co-stimulatory molecules, which improve immunogenpresentation to lymphocytes, such as B7-1 or B7-2, or cytokines such asMIP1α, GM-CSF, IL-2, and IL-12, can be included in a composition of theinvention. Optionally, adjuvants can also be included in a composition.Adjuvants are substances that can be used to nonspecifically augment aspecific immune response. Generally, an adjuvant and a polypeptide ofthe invention are mixed prior to presentation to the immune system, orpresented separately, but are presented into the same site of theanimal. Adjuvants can include, for example, oil adjuvants (e.g. Freund'scomplete and incomplete adjuvants) mineral salts (e.g. Alk(SO₄)₂;AlNa(SO₄)₂, AlNH₄(SO₄), Silica, Alum, Al(OH)₃, and Ca₃(PO₄)₂),polynucleotides (i.e. Polyic and Poly AU acids), and certain naturalsubstances (e.g. wax D from Mycobacterium tuberculosis, as well assubstances found in Corynebacterium parvum, Bordetella pertussis andmembers of the genus Brucella. Adjuvants which can be used include, butare not limited to MF59-0, aluminum hydroxide,N-acetyl-muramyl-L-threonyl-D-isoglutamine (thr-MDP),N-acetyl-nor-muramyl-L-alanyl-D-isoglutamine (CGP 11637), referred to asnor-MDP),N-acetylmuramyl-L-alanyl-D-isoglutaminyl-L-alanine-2-(I′-2′-dipamitoyl-sn-glycero-3-hydroxyphosphoryloxy)-ethylamine(CGP 19835A, referred to as MTP-PE), and RIBI, which contains threecomponents extracted from bacteria, monophosphoryl lipid A, trehalosedimycolate and cell wall skeleton (MPL+TDM+CWS) in a 2% squalene/Tween80 emulsion.

The compositions of the invention can be formulated into ingestibletablets, buccal tablets, troches, capsules, elixirs, suspensions,syrups, wafers, injectable formulations, mouthwashes, dentrifices, andthe like. The percentage of one or more polypeptides, polynucleotides,or antibodies of the invention in such compositions and preparations canvary from 0.1% to 60% of the weight of the unit.

Administration of polypeptides or polynucleotides can elicit an immuneresponse in the animal that lasts for at least 1 week, 1 month, 3months, 6 months, 1 year, or longer. Optionally, an immune response canbe maintained in an animal by providing one or more booster injectionsof the polypeptide or polynucleotide at 1 month, 3 months, 6 months, 1year, or more after the primary injection. If desired, co-stimulatorymolecules or adjuvants can also be provided before, after, or togetherwith the compositions.

A composition of the invention comprising a polypeptide, polynucleotide,or a combination thereof is administered in a manner compatible with theparticular composition used and in an amount that is effective to elicitan immune response as detected by, for example, an ELISA. Apolynucleotide can be injected intramuscularly to a large mammal, suchas a baboon, chimpanzee, or human, at a dose of 1 ng/kg, 10 ng/kg, 100ng/kg, 1000 ng/kg, 0.001 mg/kg, 0.1 mg/kg, or 0.5 mg/kg. A polypeptidecan be injected intramuscularly to a large mammal, such as a human, at adose of 0.01, 0.05, 0.5, 0.75, 1.0, 1.5, 2.0, 2.5, 5 or 10 mg/kg.

Polypeptides, polynucleotides, or antibodies, or a combination thereofcan be administered either to an animal that is not infected with Aa orcan be administered to an Aa-infected animal. The particular dosages ofpolynucleotide, polypeptides, or antibodies in a composition will dependon many factors including, but not limited to the species, age, gender,concurrent medication, general condition of the mammal to which thecomposition is administered, and the mode of administration of thecomposition. An effective amount of the composition of the invention canbe readily determined using only routine experimentation.

The materials for use in a method of the invention can be present in akit. A kit can comprise one or more elements used in the method. Forexample, a kit can contain an antibody of the invention in a containerand Aa polypeptides in another container. The kit and containers arelaled with their contents and the kit includes instructions for use ofthe elements in the containers. The constituents of the kit can bepresent in, for example, liquid or lypholized form.

All references cited in this disclosure are incorporated herein byreference.

1. A method of detecting the presence or absence of A.actinomycetemcomitans or an A. actinomycetemcomitans antigen in a testsample comprising contacting the test sample with an antibody or afragment thereof that specifically binds to a polypeptide consisting ofSEQ ID NO:146, and detecting an immunocomplex comprising A.actinomycetemcomitans or an A. actinomycetemcomitans antigen and theantibody or fragment thereof, wherein detection of the immunocomplexindicates the presence of A. actinomycetemcomitans or an A.actinomycetemcomitans antigen in the test sample.
 2. The method of claim1, wherein the test sample is plaque, saliva, crevicular fluid, sputum,blood, serum, plasma, urine, feces, cerebrospinal fluid, amniotic fluid,wound exudate, or tissue.
 3. The method of claim 1, wherein the antibodyor fragment thereof is bound to a solid substrate.
 4. The method ofclaim 1, wherein the method is an enzyme-linked immunosorbant assay(ELISA), a radioimmunoassay (RIA), or a western blot assay.
 5. A methodfor detecting an antibody specific for A. actinomycetemcomitans in atest sample comprising contacting the test sample with a purifiedpolypeptide comprising SEQ ID NO:146 and detecting formation of animmunocomplex comprising the polypeptide of SEQ ID NO:146 and theantibody specific for A. actinomycetemcomitans, wherein detection of theimmunocomplex indicates the presence of an antibody specific for A.actinomycetemcomitans in the test sample.
 6. The method of claim 5,wherein the test sample is plaque, saliva, crevicular fluid, sputum,blood, serum, plasma, urine, feces, cerebrospinal fluid, amniotic fluid,wound exudate, or tissue.
 7. The method of claim 5, wherein thepolypeptide is bound to a solid substrate.
 8. The method of to claim 5,wherein the method is an enzyme-linked immunosorbant assay (ELISA), aradioimmunoassay (RIA), or a western blot assay.